Abstract
The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care. While improvements are still expected, the techniques and the basic analytical tools have reached a state that these can be efficiently deployed in both routine research and clinical practice. Still, some major challenges remain. Notably, holistic approaches, integrating data from several sources, e.g. genomic and epigenomic, will increase the understanding of the underlying biological concepts and provide insight into the causes, effects and effective solutions. However, creating and validating such a knowledge base, potentially for different levels of expertise, and integrating several data points into meaningful information is not trivial.
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L. Van Neste, G.R. Jones, W. Van Criekinge, J.S. Clark, Personalized Medicine 8, 623 (2011)
H.M. O‘Hagan, W. Wang, S. Sen, C. Destefano Shields, S.S. Lee, Y.W. Zhang, E.G. Clements, Y. Cai, L. Van Neste, H. Easwaran, R.A. Casero, C.L. Sears, S.B. Baylin, Cancer Cell 20, 606 (2011)
J.M. Yi, M. Dhir, L. Van Neste, S.R. Downing, J. Jeschke, S.C. Glöckner, M. de Freitas Calmon, C.M. Hooker, J.M. Funes, C. Boshoff, K.M. Smits, M. van Engeland, M.P. Weijenberg, C.A. Iacobuzio-Donahue, J.G. Herman, K.E. Schuebel, S.B. Baylin, N. Ahuja, Clin. Cancer Res. 17, 1535 (2011)
L.D. Wood, D.W. Parsons, S. Jones, J. Lin, T. Sjöblom, R.J. Leary, D. Shen, S.M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P.A. Wilson, J.S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J.K.V. Willson, S. Sukumar, K. Polyak, B.H. Park, C.L. Pethiyagoda, P.V.K. Pant, D.G. Ballinger, A.B... Sparks, J. Hartigan, D.R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S.D. Markowitz, G. Parmigiani, K.W. Kinzler, V.E. Velculescu, B. Vogelstein, Science 318, 1108 (2007)
Cancer Genome Atlas Research Network, Nature 455, 1061 (2008)
P. Gaildrat, S. Krieger, D. Di Giacomo, J. Abdat, F. Révillion, S. Caputo, D. Vaur, E. Jamard, E. Bohers, D. Ledemeney, J.-P. Peyrat, C. Houdayer, E. Rouleau, R. Lidereau, T. Frébourg, A. Hardouin, M. Tosi, A. Martins, J. Med. Genet. 49, 609 (2012)
C. Mattioli, G. Pianigiani, D. De Rocco, A.M.R. Bianco, E. Cappelli, A. Savoia, F. Pagani, Biochim. Biophys. Acta 1842, 1052 (2014)
C.S. Tellez, D.E. Juri, K. Do, A.M. Bernauer, C.L. Thomas, L.A. Damiani, M. Tessema, S. Leng, S.A. Belinsky, Cancer Res. 71, 3087 (2011)
K.E. Schuebel, W. Chen, L. Cope, S.C. Glöckner, H. Suzuki, J.M. Yi, T.A. Chan, L. Van Neste, W. Van Criekinge, S. van den Bosch, M. van Engeland, A.H. Ting, K. Jair, W. Yu, M. Toyota, K. Imai, N. Ahuja, J.G. Herman, S.B. Baylin, PLoS Genet. 3, 1709 (2007)
T.A. Chan, S. Glockner, J.M. Yi, W. Chen, L. Van Neste, L. Cope, J.G. Herman, V. Velculescu, K.E. Schuebel, N. Ahuja, S.B. Baylin, PLoS Med. 5, e114 (2008)
Cancer Genome Atlas Network, Nature 487, 330 (2012)
J.G. Kim, H. Takeshima, T. Niwa, E. Rehnberg, Y. Shigematsu, Y. Yoda, S. Yamashita, R. Kushima, T. Maekita, M. Ichinose, H. Katai, W.S. Park, Y.S. Hong, C.H. Park, T. Ushijima, Cancer Lett. 330, 33 (2013)
J.M. Yi, A.A. Guzzetta, V.J. Bailey, S.R. Downing, L. Van Neste, K.B. Chiappinelli, B.P. Keeley, A. Stark, A. Herrera, C. Wolfgang, E.P. Pappou, C.A. Iacobuzio-Donahue, M.G. Goggins, J.G. Herman, T.-H. Wang, S.B. Baylin, N. Ahuja, Clin. Cancer Res. 19, 6544 (2013)
L. Van Neste, J.G. Herman, G. Otto, J.W. Bigley, J.I. Epstein, W. Van Criekinge, Prostate 72, 1248 (2012)
J. Jeschke, L. Van Neste, S.C. Glöckner, M. Dhir, M.F. Calmon, V. Deregowski, W. Van Criekinge, I. Vlassenbroeck, A. Koch, T.A. Chan, L. Cope, C.M. Hooker, K.E. Schuebel, E. Gabrielson, A. Winterpacht, S.B. Baylin, J.G. Herman, N. Ahuja, Epigenetics 7, 701 (2012)
J.G. Herman, S.B. Baylin, N. Engl, J. Med. 349, 2042 (2003)
K. Mensaert, S. Denil, G. Trooskens, W. Van Criekinge, O. Thas, T. De Meyer, Environ. Mol. Mutagen. 55, 155 (2014)
L. Van Neste, J.G. Herman, W. Van Criekinge, TJOP, 1, 29 (2013)
J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L. Gabor Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R.R. Ji, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, B. Neelam, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M.L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y.H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N.N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J.F. Abril, R. Guigó, M.J. Campbell, K.V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y.H. Chiang, M. Coyne, C. Dahlke, A. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Vent, M. Wanger, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh, X. Zhu, Science 291, 1304 (2001)
E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J.F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer, J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives, J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D.R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H.M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proctor, R.M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D.R. Cox, M.V. Olson, R. Kaul, N. Shimizu, K. Kawasaki, S. Minoshima, G.A. Evans, M. Athanasiou, R. Schultz, B.A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W.R. McCombie, M. de la Bastide, N. Dedhia, H. Blöcker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J.A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D.G. Brown, C.B. Burge, L. Cerutti, H.C. Chen, D. Church, M. Clamp, R.R. Copley, T. Doerks, S.R. Eddy, E.E. Eichler, T.S. Furey, J. Galagan, J.G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L.S. Johnson, T.A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W.J. Kent, P. Kitts, E.V. Koonin, I. Korf, D. Kulp, D. Lancet, T.M. Lowe, A. McLysaght, T. Mikkelsen, J.V. Moran, N. Mulder, V.J. Pollara, C.P. Ponting, G. Schuler, J. Schultz, G. Slater, A.F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y.I. Wolf, K.H. Wolfe, S.P. Yang, R.F. Yeh, F. Collins, M.S. Guyer, J. Peterson, A. Felsenfeld, K.A. Wetterstrand, A. Patrinos, M.J. Morgan, P. de Jong, J.J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, Y.J. Chen, J. Szustakowki, International human genome sequencing consortium. Nature 409, 860 (2001)
R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, J. Wang, Bioinformatics 25, 1966 (2009)
B. Langmead, S.L. Salzberg, Nat. Methods 9, 357 (2012)
F. Krueger, S.R. Andrews, Bioinformatics 27, 1571 (2011)
W. Guo, P. Fiziev, W. Yan, S. Cokus, X. Sun, M. Q. Zhang, P.-Y. Chen,M. Pellegrini, BMC Genomics 14, (2013)
T. Sjöblom, S. Jones, L.D. Wood, D.W. Parsons, J. Lin, T.D. Barber, D. Mandelker, R.J. Leary, J. Ptak, N. Silliman, S. Szabo, P. Buckhaults, C. Farrell, P. Meeh, S.D. Markowitz, J. Willis, D. Dawson, J.K.V. Willson, A.F. Gazdar, J. Hartigan, L. Wu, C. Liu, G. Parmigiani, B.H. Park, K.E. Bachman, N. Papadopoulos, B. Vogelstein, K.W. Kinzler, V.E. Velculescu, Science 314, 268 (2006)
C.J. Allegra, J.M. Jessup, M.R. Somerfield, S.R. Hamilton, E.H. Hammond, D.F. Hayes, P.K. McAllister, R.F. Morton, R.L. Schilsky, J. Clin. Oncol. 27, 2091 (2009)
M.S. Greenblatt, P.O. Chappuis, J.P. Bond, N. Hamel, W.D. Foulkes, Cancer Res. 61, 4092 (2001)
D. Cappellen, C. De Oliveira, D. Ricol, S. de Medina, J. Bourdin, X. Sastre-Garau, D. Chopin, J.P. Thiery, F. Radvanyi, Nat. Genet. 23, 18 (1999)
B.W. van Rhijn, I. Lurkin, F. Radvanyi, W.J. Kirkels, T.H. van der Kwast, E.C. Zwarthoff, Cancer Res. 61, 1265 (2001)
H.A. Al-Ahmadie, G. Iyer, M. Janakiraman, O. Lin, A. Heguy, S.K. Tickoo, S.W. Fine, A. Gopalan, Y.-B. Chen, A. Balar, J. Riches, B. Bochner, G. Dalbagni, D.F. Bajorin, V.E. Reuter, M.I. Milowsky, D.B. Solit, J. Pathol. 224, 270 (2011)
P. Stephens, S. Edkins, H. Davies, C. Greenman, C. Cox, C. Hunter, G. Bignell, J. Teague, R. Smith, C. Stevens, S. O‘Meara, A. Parker, P. Tarpey, T. Avis, A. Barthorpe, L. Brackenbury, G. Buck, A. Butler, J. Clements, J. Cole, E. Dicks, K. Edwards, S. Forbes, M. Gorton, K. Gray, K. Halliday, R. Harrison, K. Hills, J. Hinton, D. Jones, V. Kosmidou, R. Laman, R. Lugg, A. Menzies, J. Perry, R. Petty, K. Raine, R. Shepherd, A. Small, H. Solomon, Y. Stephens, C. Tofts, J. Varian, A. Webb, S. West, S. Widaa, A. Yates, F. Brasseur, C.S. Cooper, A.M. Flanagan, A. Green, M. Knowles, S.Y. Leung, L.H.J. Looijenga, B. Malkowicz, M.A. Pierotti, B. Teh, S.T. Yuen, A.G. Nicholson, S. Lakhani, D.F. Easton, B.L. Weber, M.R. Stratton, P.A. Futreal, R. Wooster, Nat. Genet. 37, 590 (2005)
P. Hackman, S.M. Hou, F. Nyberg, G. Pershagen, B. Lambert, Mutat. Res. 468, 45 (2000)
E. Greenberg, G. Rechavi, N. Amariglio, O. Solomon, J. Schachter, G. Markel, E. Eyal, PLoS ONE 6, e27400 (2011)
C. Tomasetti, B. Vogelstein, G. Parmigiani, Proc. Natl. Acad. Sci. U. S. A. 110, 1999 (2013)
J. Ye, A. Pavlicek, E.A. Lunney, P.A. Rejto, C.-H. Teng, BMC Bioinforma. 11, 11 (2010)
A.K. Fielding, Blood 116, 3409 (2010)
L.J.M. Mekenkamp, J.C. Haan, D. Israeli, H.F.B. van Essen, J.R. Dijkstra, P. van Cleef, C.J.A. Punt, G.A. Meijer, I.D. Nagtegaal, B. Ylstra, PLoS ONE 9, e86833 (2014)
S.J. Smeets, U. Harjes, W.N. van Wieringen, D. Sie, R.H. Brakenhoff, G.A. Meijer, B. Ylstra, Clin. Cancer Res. 17, 4959 (2011)
A.C. Wolff, M.E.H. Hammond, D.G. Hicks, M. Dowsett, L.M. McShane, K.H. Allison, D.C. Allred, J.M.S. Bartlett, M. Bilous, P. Fitzgibbons, W. Hanna, R.B. Jenkins, P.B. Mangu, S. Paik, E.A. Perez, M.F. Press, P.A. Spears, G.H. Vance, G. Viale, D.F. Hayes, American society of clinical oncology, college of american pathologists. J. Clin. Oncol. 31, 3997 (2013)
M. Esteller, J. Garcia-Foncillas, E. Andion, S.N. Goodman, O.F. Hidalgo, V. Vanaclocha, S.B. Baylin, J.G. Herman, N. Engl, J. Med. 343, 1350 (2000)
M. Esteller, S.R. Hamilton, P.C. Burger, S.B. Baylin, J.G. Herman, Cancer Res. 59, 793 (1999)
M.E. Hegi, A.-C. Diserens, T. Gorlia, M.-F. Hamou, N. de Tribolet, M. Weller, J.M. Kros, J.A. Hainfellner, W. Mason, L. Mariani, J.E.C. Bromberg, P. Hau, R.O. Mirimanoff, J.G. Cairncross, R.C. Janzer, R. Stupp, N. Engl, J. Med. 352, 997 (2005)
I.J.H. van Vlodrop, H.E.C. Niessen, S. Derks, M.M.L.L. Baldewijns, W. Van Criekinge, J.G. Herman, M. van Engeland, Clin. Cancer Res. 17, 4225 (2011)
J.G. Herman, J.R. Graff, S. Myöhänen, B.D. Nelkin, S.B. Baylin, Proc. Natl. Acad. Sci. U. S. A. 93, 9821 (1996)
I. Vlassenbroeck, S. Califice, A.-C. Diserens, E. Migliavacca, J. Straub, I. Di Stefano, F. Moreau, M.-F. Hamou, I. Renard, M. Delorenzi, B. Flamion, J. DiGuiseppi, K. Bierau, M.E. Hegi, J. Mol. Diagn. 10, 332 (2008)
J.C. Rice, K.S. Massey-Brown, B.W. Futscher, Oncogene 17, 1807 (1998)
T. Hansmann, G. Pliushch, M. Leubner, P. Kroll, D. Endt, A. Gehrig, S. Preisler-Adams, P. Wieacker, T. Haaf, Hum. Mol. Genet. 21, 4669 (2012)
A. Meissner, A. Gnirke, G.W. Bell, B. Ramsahoye, E.S. Lander, R. Jaenisch, Nucleic Acids Res. 33, 5868 (2005)
D. Serre, B.H. Lee, A.H. Ting, Nucleic Acids Res. 38, 391 (2010)
T. De Meyer, E. Mampaey, M. Vlemmix, S. Denil, G. Trooskens, J.-P. Renard, S. De Keulenaer, P. Dehan, G. Menschaert, W. Van Criekinge, PLoS ONE 8, e59068 (2013)
B.P. Berman, D.J. Weisenberger, J.F. Aman, T. Hinoue, Z. Ramjan, Y. Liu, H. Noushmehr, C.P.E. Lange, C.M. van Dijk, R.A.E.M. Tollenaar, D. Van Den Berg, P.W. Laird, Nat. Genet. 44, 40 (2012)
M. Sultan, M.H. Schulz, H. Richard, A. Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk, D. Schmidt, S. O‘Keeffe, S. Haas, M. Vingron, H. Lehrach, M.-L. Yaspo, Science 321, 956 (2008)
1000 Genomes Project Consortium, G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean, Nature 467, 1061 (2010)
G. Menschaert, W. Van Criekinge, T. Notelaers, A. Koch, J. Crappé, K. Gevaert, P. Van Damme, Mol. Cell. Proteomics 12, 1780 (2013)
P. Flicek, M.R. Amode, D. Barrell, K. Beal, K. Billis, S. Brent, D. Carvalho-Silva, P. Clapham, G. Coates, S. Fitzgerald, L. Gil, C.G. Giron, L. Gordon, T. Hourlier, S. Hunt, N. Johnson, T. Juettemann, A.K. Kaehaeri, S. Keenan, E. Kulesha, F.J. Martin, T. Maurel, W.M. McLaren, D.N. Murphy, R. Nag, B. Overduin, M. Pignatelli, B. Pritchard, E. Pritchard, H.S. Riat, M. Ruffier, D. Sheppard, K. Taylor, A. Thormann, S.J. Trevanion, A. Vullo, S.P. Wilder, M. Wilson, A. Zadissa, B.L. Aken, E. Birney, F. Cunningham, J. Harrow, J. Herrero, T.J.P. Hubbard, R. Kinsella, M. Muffato, A. Parker, G. Spudich, A. Yates, D.R. Zerbino, S.M.J. Searle, Nucleic Acids Res. 42, D749 (2014)
R.M. Kuhn, D. Haussler, W.J. Kent, Brief. Bioinforma. 14, 144 (2013)
J. Goecks, A. Nekrutenko, J. Taylor, G. Team, Genome Biol. 11, (2010)
J. Wrangle, E.O. Machida, L. Danilova, A. Hulbert, N. Franco, W. Zhang, S.C. Glöckner, M. Tessema, L. Van Neste, H. Easwaran, K.E. Schuebel, J. Licchesi, C.M. Hooker, N. Ahuja, J. Amano, S.A. Belinsky, S.B. Baylin, J.G. Herman, M.V. Brock, Clin. Cancer Res. 20, 1856 (2014)
D.L. Wheeler, D.M. Church, A.E. Lash, D.D. Leipe, T.L. Madden, J.U. Pontius, G.D. Schuler, L.M. Schriml, T.A. Tatusova, L. Wagner, B.A. Rapp, Nucleic Acids Res. 29, 11 (2001)
A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra, S.-A. Sansone, Nucleic Acids Res. 31, 68 (2003)
A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron, Nat. Genet. 29, 365 (2001)
R. Leinonen, H. Sugawara, M. Shumway, International nucleotide sequence database collaboration. Nucleic Acids Res. 39, D19 (2011)
W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, D. Haussler, Genome Res. 12, 996 (2002)
T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik, M. Clamp, Nucleic Acids Res. 30, 38 (2002)
Nat. Methods 5, 989 (2008)
N.R. Wray, J. Yang, B.J. Hayes, A.L. Price, M.E. Goddard, P.M. Visscher, Nat. Rev. Genet. 14, 507 (2013)
N.R. Wray, M.E. Goddard, P.M. Visscher, Genome Res. 17, 1520 (2007)
M.F. Fraga, E. Ballestar, M.F. Paz, S. Ropero, F. Setien, M.L. Ballestar, D. Heine-Suñer, J.C. Cigudosa, M. Urioste, J. Benitez, M. Boix-Chornet, A. Sanchez-Aguilera, C. Ling, E. Carlsson, P. Poulsen, A. Vaag, Z. Stephan, T.D. Spector, Y.-Z. Wu, C. Plass, M. Esteller, Proc. Natl. Acad. Sci. U. S. A. 102, 10604 (2005)
P. Poulsen, M. Esteller, A. Vaag, M.F. Fraga, Pediatr. Res. 61, 38R (2007)
International Human Genome Sequencing Consortium, Nature 431, 931 (2004)
A.H.C. Wong, I.I. Gottesman, A. Petronis, Hum. Mol. Genet. 14(Spec No 1), R11 (2005)
R. Yoshida, M. Nakajima, Y. Watanabe, J.-T. Kwon, T. Yokoi, Br. J. Clin. Pharmacol. 54, 511 (2002)
C. Rodríguez-Antona, M. Niemi, J.T. Backman, L.I. Kajosaari, P.J. Neuvonen, M. Robledo, M. Ingelman-Sundberg, Pharmacogenomics J. 8, 268 (2008)
M. Wadelius, L.Y. Chen, J.D. Lindh, N. Eriksson, M.J.R. Ghori, S. Bumpstead, L. Holm, R. McGinnis, A. Rane, P. Deloukas, Blood 113, 784 (2009)
J. de Leon, M.T. Susce, R.-M. Pan, M. Fairchild, W.H. Koch, P.J. Wedlund, J. Clin. Psychiatry 66, 15 (2005)
L. Pierret, N.V. Baren, A. Bonehill, J. Corthals, A.M.T. Van Nuffel, C. Heirman, T. Roelandt, A. De Coninck, I.V. Riet, E. Degreef, A. Goossens, G. Verfaillie, D. Roseeuw, K. Thielemans, B. Neyns, Melanoma Res. 19, 385 (2009)
A. Bonehill, A.M.T. Van Nuffel, J. Corthals, S. Tuyaerts, C. Heirman, V. François, D. Colau, P. van der Bruggen, B. Neyns, K. Thielemans, Clin. Cancer Res. 15, 3366 (2009)
F. Ulloa-Montoya, J. Louahed, B. Dizier, O. Gruselle, B. Spiessens, F.F. Lehmann, S. Suciu, W.H.J. Kruit, A.M.M. Eggermont, J. Vansteenkiste, V.G. Brichard, J. Clin. Oncol. 31, 2388 (2013)
M. Rajasagi, S. A. Shukla, E. F. Fritsch, D. B. Keskin, D. DeLuca, E. Carmona, W. Zhang, C. Sougnez, K. Cibulskis, J. Sidney, K. Stevenson, J. Ritz, D. Neuberg, V. Brusic, S. Gabriel, E. S. Lander, G. Getz, N. Hacohen, and C. J. Wu, Blood (2014)
S. Schwartz, I. Friedberg, I.V. Ivanov, L.A. Davidson, J.S. Goldsby, D.B. Dahl, D. Herman, M. Wang, S.M. Donovan, R.S. Chapkin, Genome Biol. 13, r32 (2012)
P. Lepage, M.C. Leclerc, M. Joossens, S. Mondot, H.M. Blottière, J. Raes, D. Ehrlich, J. Doré, Gut 62, 146 (2013)
M. C. Cénit, V. Matzaraki, E. F. Tigchelaar, and A. Zhernakova, Biochim. Biophys. Acta (2014)
J. Jeschke, H.M. O‘Hagan, W. Zhang, R. Vatapalli, M.F. Calmon, L. Danilova, C. Nelkenbrecher, L. Van Neste, I.T.G.W. Bijsmans, M. van Engeland, E. Gabrielson, K.E. Schuebel, A. Winterpacht, S.B. Baylin, J.G. Herman, N. Ahuja, Clin. Cancer Res. 19, 3201 (2013)
G.D. Stewart, L. Van Neste, P. Delvenne, P. Delrée, A. Delga, S.A. McNeill, M. O‘Donnell, J. Clark, W. Van Criekinge, J. Bigley, D.J. Harrison, J. Urol. 189, 1110 (2013)
A. W. Partin, L. Van Neste, E. A. Klein, L. S. Marks, J. R. Gee, D. A. Troyer, K. Rieger-Christ, J. S. Jones, C. Magi-Galluzzi, L. A. Mangold, B. J. Trock, R. S. Lance, J. W. Bigley, W. Van Criekinge, and J. I. Epstein, J. Urol. (2014)
S.C. Glöckner, M. Dhir, J.M. Yi, K.E. McGarvey, L. Van Neste, J. Louwagie, T.A. Chan, W. Kleeberger, A.P. de Bruïne, K.M. Smits, C.A.J. Khalid-de Bakker, D.M.A.E. Jonkers, R.W. Stockbrügger, G.A. Meijer, F.A. Oort, C. Iacobuzio-Donahue, K. Bierau, J.G. Herman, S.B. Baylin, M. van Engeland, K.E. Schuebel, N. Ahuja, Cancer Res. 69, 4691 (2009)
V. Melotte, M.H.F.M. Lentjes, S.M. van den Bosch, D.M.E.I. Hellebrekers, J.P.J. de Hoon, K.A.D. Wouters, K.L.J. Daenen, I.E.J.M. Partouns-Hendriks, F. Stessels, J. Louwagie, K.M. Smits, M.P. Weijenberg, S. Sanduleanu, C.A.J. Khalid-de Bakker, F.A. Oort, G.A. Meijer, D.M.A.E. Jonkers, J.G. Herman, A.P. de Bruïne, M. van Engeland, J. Natl. Cancer Inst. 101, 916 (2009)
T.F. Imperiale, D.F. Ransohoff, S.H. Itzkowitz, T.R. Levin, P. Lavin, G.P. Lidgard, D.A. Ahlquist, B.M. Berger, N. Engl, J. Med. 370, 1287 (2014)
C. Bettegowda, M. Sausen, R.J. Leary, I. Kinde, Y. Wang, N. Agrawal, B.R. Bartlett, H. Wang, B. Luber, R.M. Alani, E.S. Antonarakis, N.S. Azad, A. Bardelli, H. Brem, J.L. Cameron, C.C. Lee, L.A. Fecher, G.L. Gallia, P. Gibbs, D. Le, R.L. Giuntoli, M. Goggins, M.D. Hogarty, M. Holdhoff, S.-M. Hong, Y. Jiao, H.H. Juhl, J.J. Kim, G. Siravegna, D.A. Laheru, C. Lauricella, M. Lim, E.J. Lipson, S.K.N. Marie, G.J. Netto, K.S. Oliner, A. Olivi, L. Olsson, G.J. Riggins, A. Sartore-Bianchi, K. Schmidt, L.-M. Shih, S.M. Oba-Shinjo, S. Siena, D. Theodorescu, J. Tie, T.T. Harkins, S. Veronese, T.-L. Wang, J.D. Weingart, C.L. Wolfgang, L.D. Wood, D. Xing, R.H. Hruban, J. Wu, P.J. Allen, C.M. Schmidt, M.A. Choti, V.E. Velculescu, K.W. Kinzler, B. Vogelstein, N. Papadopoulos, L.A. Diaz, Sci. Transl. Med. 6, 224ra24 (2014)
J. Wrangle, W. Wang, A. Koch, H. Easwaran, H.P. Mohammad, F. Vendetti, W. Vancriekinge, T. Demeyer, Z. Du, P. Parsana, K. Rodgers, R.-W. Yen, C.A. Zahnow, J.M. Taube, J.R. Brahmer, S.S. Tykodi, K. Easton, R.D. Carvajal, P.A. Jones, P.W. Laird, D.J. Weisenberger, S. Tsai, R.A. Juergens, S.L. Topalian, C.M. Rudin, M.V. Brock, D. Pardoll, S.B. Baylin, Oncotarget 4, 2067 (2013)
R.A. Juergens, J. Wrangle, F.P. Vendetti, S.C. Murphy, M. Zhao, B. Coleman, R. Sebree, K. Rodgers, C.M. Hooker, N. Franco, B. Lee, S. Tsai, I.E. Delgado, M.A. Rudek, S.A. Belinsky, J.G. Herman, S.B. Baylin, M.V. Brock, C.M. Rudin, Cancer Discov. 1, 598 (2011)
M.L. de Groote, P.J. Verschure, M.G. Rots, Nucleic Acids Res. 40, 10596 (2012)
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Van Neste, L., Van Criekinge, W. We are all individuals… bioinformatics in the personalized medicine era. Cell Oncol. 38, 29–37 (2015). https://doi.org/10.1007/s13402-014-0195-3
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DOI: https://doi.org/10.1007/s13402-014-0195-3